Aha! I knew there was a better way of doing this, but I was stuck on a
machine that only had an old version of PyMOL. Assuming you're using PyMOL
1.0 or newer, you can just use pseudoatom. To create a sphere of radius 10.0
at the xyz position (50.0,60.0,12.0), just do this:
pseudoatom mysphere, pos=[50.0,60.0,12.0], vdw=[10.0]
it will appear as a kind of cross at first. to show it as a sphere, type
show spheres, mysphere
to make it partially transparent, type
set sphere_transparency, 0.5, mysphere
The sphere that you get will look kind of blocky. You can get a perfect
sphere by raytracing, e.g. typing
ray
If you don't mind the fact that it won't be transparent, you can get a
perfect sphere in the normal viewer by typing
set sphere_mode, 5
To go back to normal spheres after you've done that, type
unset sphere_mode
I think this will be easier than the other way I recommended.
Cheers,
-michael
On Tue, Jul 7, 2009 at 1:55 PM, Benjamin Michael Owen
<owe...@marshall.edu>wrote:
> I'm trying to use a suggestion another pymol user sent to create a sphere
> of a specific size in a pdb file. Is this the correct coding? I have no
> experience doing any kind of programming so I am not sure if I did this
> right. I put the text I entered in in red if that helps anything.
>
> ben
>
> create sphere, resi 24 and resi 864 create a new object from resi 864
>
> alter sphere, vdw=10.0 # 28.5
>
> rebuild # necessary if spheres have already been shown
>
> show spheres, sphere
>
> alter_state 1, sphere, x,y,z = 50,60,10 # set desired x,y,z coords
>
> set sphere_transparency, 0.5, sphere # make it transparent
>
> zoom
>
> ray
>
>
> ------------------------------------------------------------------------------
> Enter the BlackBerry Developer Challenge
> This is your chance to win up to $100,000 in prizes! For a limited time,
> vendors submitting new applications to BlackBerry App World(TM) will have
> the opportunity to enter the BlackBerry Developer Challenge. See full prize
> details at: http://p.sf.net/sfu/blackberry
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
------------------------------------------------------------------------------
Enter the BlackBerry Developer Challenge
This is your chance to win up to $100,000 in prizes! For a limited time,
vendors submitting new applications to BlackBerry App World(TM) will have
the opportunity to enter the BlackBerry Developer Challenge. See full prize
details at: http://p.sf.net/sfu/blackberry
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
